While there is valid dispute between liberal cubing, API tools, etc and whether it adds or detracts from the game I think we can all agree in many areas globally faction balance (or lack there of) are is generally accepted as a negative.
Rather than just say "ZOMG BBQ FIX PLZ THX BYE!" I decided to write up my views / suggestions...
The problem:
The basic problem is as time marches on areas are becoming more and more one sided in number of active players in one faction over the others. (This problem is not exclusive to any one faction or location.
Why is this a problem:
The short version is it's no fun for either side long term, results in people quitting, and also stops the need/desire to cube which is how QONQR makes money.
Negative for faction in power:
Once the balance tips past a certain point the opposition is no longer able to fight on a real level and are forced to tower or just surrender their zones. Short term grinding away enemy territory can be fun, but long term you find yourself with no challenge. You just knock out zones in what feels like just another day. No strategy needed, you have such numbers you just brute force with no further thought. After that you run out of enemies and are left with nothing to do but nano missile remote targets and stack your zones. Eventually you get bored and probably quit.
Negative for out numbered faction:
When the tipping point is past no level of amazing strategy will be enough to defeat the raw numbers. The enemy can take back in minutes what you spend hours to take, and no level of organized defense will stop you from losing zones. Eventually you WILL be wiped out and you know it. Eventually you stop caring, shortly after you quit because your efforts are meaningless against a so heavily stacked situation.
Why does this stop cubing:
Some cubing will continue but general once cubing becomes unnecessary for the larger force to topple towers they stop doing so. At the same hand while a defender might turn to cubing short term once you pass the tipping point you quickly realize cubing isn't a maintainable strategy and you are doomed to fall. At this point you stop bothering and QONQR's income in your region dries up.
How did we get here?
The primary reason we got here was both game mechanics and human nature encourage stacking. Here are the factors that promote stacking.
You generate more credits based on who controls an area, if someone is clearly winning it makes strategic sense to join them.
Majority prefer to win. While not all people like to join the winning team generally speaking more people will join those in power than others
Recruitment power. More players on a faction is more people capable of recruiting so better return totals
Chilling effect. The force in power can easily swat new players in areas they control resulting in low new player retention or causing that player to switch factions perpetuating the problem.
Backstories. While a lesser factor different demographics cater more towards different back stories as such areas that have a heavy tendency towards certain ideals tend to favor different factions more.
There Are some factors that work against stacking but not as strong, here are some examples in favor of balance
Underdog mentality. There is a minority of players who prefer to play the underdog this helps balance, unfortunately this is directly countered by he prefer to win issue.
Boredom, from time to time a larger faction will suffer defection out of boredom. Unfortunately when things reach this point the balance is already so far out of tolerance the new recruit finds themselves incapable of doing anything
What can be done?
The short version is make changes to the game mechanics to encourage or if necessary force balance with in a certain tolerance. (Force would be a last resort)
Some Options and their pros and cons:
Remove starting alliance choice and just set the new player to the least active. This has the pro of the preventing the back story from influencing the choice to much, but is won't likely have only a trivial impact.
Remove the credit benefit from friendly bases. The pro is now territory control doesn't effect your resources making it less strategic to join the winning team. the con is there's no benefit from holding territory
Create a Penalty on disproportionally large faction in an area. (we're not taking 1:2 we're talking in excess of 1:3) The penalty could be credit generation, survivability, defense, offense, heat, combination. The exact penalty amount would have to be proportion to the factions disproportion. Pros, allows the smaller force a little more wiggle room before numbers win, encourages players to switch down. Cons, This could be seen as unfair and could cause excessive faction flipping to dodge penalties while trying to stay with friends.
Create a perk on disproportionally small faction in an area. (effectively a reversal of the penalty with the same basic pros and cons)
Create a penalty for switching to a larger faction. Temporarily causes the individual a significant penalty such as those mentioned above. Pros a bit more fair than an across the board penalty, but if too short becomes in effective. Cons same basic cons as the across the board, but mitigated slightly.
Create a perk for switching to a smaller faction. The reversal of the switching penalty with the same basic pros and cons.
Disallow switching to a faction that's disproportionally large. Pros assuming players stay this WILL force balance Cons player retention could still be terrible mitigating it's effectiveness but more importantly it could prevent family and friends from playing together.
There are plenty of other options, all with pros and cons, but ultimately it's do nothing and watch more and more areas become unbalanced and effectively stack offs (or vacant) at a reduced income to QONQR. Or do something knowing it will **** people off but could help improve general activity and closer to even combat in an area (which means more cubing and income to QONQR)

The Faceless's flames are derived from the Greek myth about the titan Promethus stealing fire from the gods and giving it to humans. I have no idea what Swarm's infinity and Legion's shield mean, though.

What are the pros and cons of doing so? I'm a level 62 with 2 level 90 faceless players in my area, when I first started playing it was fun because there was a large swarm presence in our area; but we have since wiped them from the map. I've been considering switching sides to get the achievements and to switch the game up here. Also incentives from other factions are welcome I suppose, I've already been offered a nice chunk of cubes by a swarm agent in my area. Just saying.